Deep sequencing of mycovirus‐derived small RNAs from Botrytis species

RNA silencing is an ancient regulatory mechanism operating in all eukaryotic cells. In fungi, it was first discovered in Neurospora crassa, although its potential as a defence mechanism against mycoviruses was first reported in Cryphonectria parasitica and, later, in several fungal species. There is little evidence of the antiviral potential of RNA silencing in the phytopathogenic species of the fungal genus Botrytis. Moreover, little is known about the RNA silencing components in these fungi, although the analysis of public genome databases identified two Dicer‐like genes in B. cinerea, as in most of the ascomycetes sequenced to date. In this work, we used deep sequencing to study the virus‐derived small RNA (vsiRNA) populations from different mycoviruses infecting field isolates of Botrytis spp. The mycoviruses under study belong to different genera and species, and have different types of genome [double‐stranded RNA (dsRNA), (+)single‐stranded RNA (ssRNA) and (–)ssRNA]. In general, vsiRNAs derived from mycoviruses are mostly of 21, 20 and 22 nucleotides in length, possess sense or antisense orientation, either in a similar ratio or with a predominance of sense polarity depending on the virus species, have predominantly U at their 5′ end, and are unevenly distributed along the viral genome, showing conspicuous hotspots of vsiRNA accumulation. These characteristics reveal striking similarities with vsiRNAs produced by plant viruses, suggesting similar pathways of viral targeting in plants and fungi. We have shown that the fungal RNA silencing machinery acts against the mycoviruses used in this work in a similar manner independent of their viral or fungal origin.     

Family matters: How MYC family oncogenes impact small cell lung cancer

Small cell lung cancer (SCLC) is one of the most deadly cancers and currently lacks effective targeted treatment options. Recent advances in the molecular characterization of SCLC has provided novel insight into the biology of this disease and raises hope for a paradigm shift in the treatment of SCLC. We and others have identified activation of MYC as a driver of susceptibility to Aurora kinase inhibition in SCLC cells and tumors that translates into a therapeutic option for the targeted treatment of MYC-driven SCLC. While MYC shares major features with its paralogs MYCN and MYCL, the sensitivity to Aurora kinase inhibitors is unique for MYC-driven SCLC. In this review, we will compare the distinct molecular features of the 3 MYC family members and address the potential implications for targeted therapy of SCLC.     

hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA

Human NUDT16 (hNUDT16) is a decapping enzyme initially identified as the human homolog to the Xenopus laevis X29. As a metalloenzyme, hNUDT16 relies on divalent cations for its cap-hydrolysis activity to remove m⁷GDP and m²²⁷GDP from RNAs. Metal also determines substrate specificity of the enzyme. So far, only U8 small nucleolar RNA (snoRNA) has been identified as the substrate of hNUDT16 in the presence of Mg²⁺. Here we demonstrate that besides U8, hNUDT16 can also actively cleave the m⁷GDP cap from mRNAs in the presence of Mg²⁺ or Mn²⁺. We further show that hNUDT16 does not preferentially recognize U8 or mRNA substrates by our cross-inhibition and quantitative decapping assays. In addition, our mutagenesis analysis identifies several key residues involved in hydrolysis and confirms the key role of the REXXEE motif in catalysis. Finally an investigation into the subcellular localization of hNUDT16 revealed its abundance in both cytoplasm and nucleus. These findings extend the substrate spectrum of hNUDT16 beyond snoRNAs to also include mRNA, demonstrating the pleiotropic decapping activity of hNUDT16.     

Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus

Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3′-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII_170–755, as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.     

Chancelloriid sclerites from the Lower Cambrian (Meishucunian) of eastern Yunnan,China, and the early history of the group

Chancelloriids are a group of enigmatic sessile animals that are covered with sclerites shaped as rosettes of spines, producing an appearance like that of a barrel cactus. They are known only from Cambrian rocks. Isolated sclerites of chancelloriids are widespread in small shelly faunas, but they have proven difficult to treat taxonomically due to the variation within and between individual animals. We report on large samples of chancelloriid sclerites from the Meishucunian (pre‐trilobitic Lower Cambrian) of eastern Yunnan Province, China, including material from the Dahai Member of the Zhujiaqing Formation (the Zhujiaqing section, Dahai, Huize County) and the Shiyantou Formation (the Xiaotan section, Yongshan County). The material from the Dahai Member appears to come from a single species, Chancelloriella irregularis. Statistical analysis of morphotype co‐occurrences in different samples suggests that several species are represented in the material from the Shiyantou Formation, which we herein tentatively place in four species, Allonnia erromenosa, Allonnia tetrathallis, Archiasterella charma sp. nov. and Archiasterella cf. pentactina. We suggest therefore that careful study of large collections of isolated chancelloriid sclerites permits the identification of different species, opening the possibility of their use in evolutionary or stratigraphical studies. In particular, in South China, it seems that Chancelloriella irregularis is characteristic of rocks of the Paragloborilus subglobosus – Purella squamulosa Assemblage Zone and the Watsonella crosbyi Assemblage Zone, whilst Archiasterella and Allonnia first appear in the overlying Sinosachites flabelliformis – Tannuolina zhangwentangi Assemblage Zone. C. irregularis is thus amongst the oldest well‐characterized chancelloriids, and the irregularity and poor organization of its sclerites relative to those of younger forms support the hypothesis that chancelloriid sclerites are compound structures arising from the fusion of originally separate elements, perhaps homologous with sclerites of halkieriids and other coeloscleritophorans. The similarity between the arrangement of rays in a chancelloriid sclerite and the arrangement of bubbles in small bubble clusters suggests that in many cases, aspects of the form of chancelloriid sclerites are the result of simple physical processes.     

Study of interactions between DNA and aflatoxin B1 using electrochemical and fluorescence methods

In this study, a carbon paste electrode modified with N-butylpyridinium hexafluorophosphate (BPPF₆) ionic liquid and DNA was introduced as an electrochemical biosensor to study the interaction between DNA and aflatoxin B1 molecules. For this purpose, variations in oxidation peak current of guanine in various concentrations of aflatoxin B1 were measured by using the differential pulse voltammetry (DPV) method. According to this study, the binding constant of DNA–aflatoxin B1 was found to be 3.5 × 10⁶ M⁻¹. This modified electrode was also used for determination of low concentrations of aflatoxin B1 by using differential pulse voltammetry. A linear dynamic range from 8.00 × 10⁻⁸ to 5.91 × 10⁻⁷ M and a limit of detection of 2.00 × 10⁻⁸ M resulted from DPV measurements. To confirm our results, a fluorescence study was also performed. It resulted in a binding constant of 2.8 × 10⁶ M⁻¹, which is in good agreement with that obtained from electrochemical study.